This document outlines plans for multi-site sequencing studies to generate standardized human and bacterial genome sequencing datasets. Samples include a human trio, bacterial isolates, and mixtures, which will be sequenced in triplicate across three sites on various platforms including Illumina HiSeq X Ten, HiSeq 4000, HiSeq 2500, NextSeq 500, Life Tech Ion Proton, Ion S5, Pacific Biosciences, Oxford Nanopore, and others. The goals are to measure intra- and inter-lab variation, sequencing performance at GC extremes, and establish molecular standards for assessing sequencing methods in DNA, RNA, and metagenomics. Data will be analyzed by a team to benchmark tools and published by October 2017.
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
Building an Information Infrastructure to Support Microbial Metagenomic SciencesLarry Smarr
06.01.14
Presentation for the Microbe Project Interagency Team
Title: Building an Information Infrastructure to Support Microbial Metagenomic Sciences
La Jolla, CA
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Tools for Metagenomics with 16S/ITS and Whole Genome Shotgun SequencesSurya Saha
Presented at Cornell Symbiosis symposium. Workflow for processing amplicon based 16S/ITS sequences as well as whole genome shotgun sequences are described. Slides include short description and links for each tool.
DISCLAIMER: This is a small subset of tools out there. No disrespect to methods not mentioned.
The Emerging Global Collaboratory for Microbial Metagenomics ResearchersLarry Smarr
08.07.30
Invited Talk
Delivered From Calit2@UCSD
Monash University MURPA Lecture
Title: The Emerging Global Collaboratory for Microbial Metagenomics Researchers
Melbourne, Australia
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Phylogenomic methods for comparative evolutionary biology - University Colleg...Joe Parker
Invited research seminar given to MSc students at University College Dublin on 24th October 2013.
I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field.
As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals.
I then highlight some of the avenues of study on the frontiers of current research.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSLubna MRL
After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed.
Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Building an Information Infrastructure to Support Microbial Metagenomic SciencesLarry Smarr
06.01.14
Presentation for the Microbe Project Interagency Team
Title: Building an Information Infrastructure to Support Microbial Metagenomic Sciences
La Jolla, CA
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Tools for Metagenomics with 16S/ITS and Whole Genome Shotgun SequencesSurya Saha
Presented at Cornell Symbiosis symposium. Workflow for processing amplicon based 16S/ITS sequences as well as whole genome shotgun sequences are described. Slides include short description and links for each tool.
DISCLAIMER: This is a small subset of tools out there. No disrespect to methods not mentioned.
The Emerging Global Collaboratory for Microbial Metagenomics ResearchersLarry Smarr
08.07.30
Invited Talk
Delivered From Calit2@UCSD
Monash University MURPA Lecture
Title: The Emerging Global Collaboratory for Microbial Metagenomics Researchers
Melbourne, Australia
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Phylogenomic methods for comparative evolutionary biology - University Colleg...Joe Parker
Invited research seminar given to MSc students at University College Dublin on 24th October 2013.
I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field.
As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals.
I then highlight some of the avenues of study on the frontiers of current research.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSLubna MRL
After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed.
Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy.
Data Management for Quantitative Biology - Data sources (Next generation tech...QBiC_Tue
Introduction to next generation sequencing (NGS); NGS data; data management of NGS data; third generation sequencing; NGS pipelines; NGS experimental design
ICAR 2015
Workshop 10 (TUESDAY, JULY 7, 2015, 4:30-6:00 PM)
The Arabidopsis information portal for users and developers
Nick Provart (University of Toronto)
A Community Collaborator Perspective: Case study 1 - BioAnalytic Resource
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Databasenist-spin
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Lisa Johnson at #ICG13: Re-assembly, quality evaluation, and annotation of 67...GigaScience, BGI Hong Kong
Lisa Johnson's talk at the #ICG13 GigaScience Prize Track: Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Shenzhen, 26th October 2018
The prostate is an exocrine gland of the male mammalian reproductive system
It is a walnut-sized gland that forms part of the male reproductive system and is located in front of the rectum and just below the urinary bladder
Function is to store and secrete a clear, slightly alkaline fluid that constitutes 10-30% of the volume of the seminal fluid that along with the spermatozoa, constitutes semen
A healthy human prostate measures (4cm-vertical, by 3cm-horizontal, 2cm ant-post ).
It surrounds the urethra just below the urinary bladder. It has anterior, median, posterior and two lateral lobes
It’s work is regulated by androgens which are responsible for male sex characteristics
Generalised disease of the prostate due to hormonal derangement which leads to non malignant enlargement of the gland (increase in the number of epithelial cells and stromal tissue)to cause compression of the urethra leading to symptoms (LUTS
Report Back from SGO 2024: What’s the Latest in Cervical Cancer?bkling
Are you curious about what’s new in cervical cancer research or unsure what the findings mean? Join Dr. Emily Ko, a gynecologic oncologist at Penn Medicine, to learn about the latest updates from the Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer. Dr. Ko will discuss what the research presented at the conference means for you and answer your questions about the new developments.
Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
Factory Supply Best Quality Pmk Oil CAS 28578–16–7 PMK Powder in Stockrebeccabio
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Anti ulcer drugs and their Advance pharmacology ||
Anti-ulcer drugs are medications used to prevent and treat ulcers in the stomach and upper part of the small intestine (duodenal ulcers). These ulcers are often caused by an imbalance between stomach acid and the mucosal lining, which protects the stomach lining.
||Scope: Overview of various classes of anti-ulcer drugs, their mechanisms of action, indications, side effects, and clinical considerations.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
Cross-Kingdom Standards in Genomics, Epigenomics and Metagenomics
1. Cross-Kingdom Standards in Genomics,
Epigenomics and Metagenomics
(for this world and maybe others)
Christopher E. Mason, Ph.D.
Associate Professor
Department of Physiology and Biophysics &
The Institute for Computational Biomedicine (ICB),
Meyer Cancer Center, Feil Family Brain and Mind Research Institute,
at Weill Cornell Medicine,
Fellow of the Information Society Project, Yale Law School
June 29th , 2017
8. Acronym Group Type Agency/GroupWeb site(s) for Consortiums, Data Sets, Methods, and/or Materials
GIAB Genome in a Bottle
DNA and
cells
NIST https://sites.stanford.edu/abms/giab
Nex-StoCT
Next-generation Sequencing: Standardization of
Clinical Testing (Nex-StoCT) II
DNA CDC http://www.cdc.gov/ophss/csels/dlpss/Genetic_Testing_Quality_Practices/ngsqp.html
GeT-RM
Genetic Testing Reference Materials
Coordination Program
DNA CDC http://wwwn.cdc.gov/clia/Resources/GetRM/default.aspx
http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/
http://www.nature.com/nbt/collections/seqc/index.html
http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/
http://www.nature.com/nbt/focus/maqc/index.html
http://www.abrf.org/index.cfm/group.show/NextGenerationSequencing%28NGS%29.75.htm
http://www.biotech.cornell.edu/news/abrf-next-generation-sequencing-study-webinar
GEUVADIS Genetic European Variation in Health and DiseaseRNA EU http://www.geuvadis.org
http://www.nist.gov/mml/bbd/ercc.cfm
https://www.lifetechnologies.com/order/catalog/product/4456740
ERCC2 External RNA Control Consortium 2 RNA NIST http://www.nist.gov/mml/bbd/ercc2.cfm
SIRV Spike-In RNA Variant Mixes RNA Lexigen https://www.lexogen.com/sirvsrelease/
MBQC Microbiome Quality Control Consortium meta MBQC www.mbqc.org
IMMSA
International Metagenomics and Microbiome
Standards Consortium
meta NIST http://www.nist.gov/mml/bbd/microbial_metrology/immsa-mission-statement.cfm
IHMS International Human Microbiome Standardsmeta meta www.microbiome-standards.org/
BiOMICs Bio-OMICS mixed kingdom DNA standard
meta
and cells
Zymo http://www.zymobiomics.com/
ATCC
International Metagenomics and Microbiome
Standards Consortium
meta ATCC http://www.atcc.org/products/all/CCL-186.aspx
BEI International Human Microbiome Standardsmeta NIAID https://www.beiresources.org/Catalog/otherProducts/HM-782D.aspx
EMP Earth Microbiome Project meta EMP http://earthmicrobiome.org/
XMP eXtreme Microbiome Project meta XMP http://extrememicrobiome.org/
MGRG Metagenomics Research Group meta ABRF http://blog.abrf.org/
MetaSUB
International Metagenomics and Metadesign of
Subways and Urban Biomes
meta ABRF http://www.metasub.org
MAQC / MAQC2
SEQC / SEQC2
Microarray Quality Control Consortium
Sequencing Quality Control Consortium
ABRF-NGS
Registry of Standard Biological Parts DNA iGEM
genome/epigenome
ABRF
Association of Biomolecular Resource Facilities
(ABRF) Next-generation Sequencing
RNA
FDA
transcriptome/epitranscriptome
RNA
metagenome/metatranscriptome
Molecular Standards for Assessing Library, Sequencing, and Analysis Methods in DNA, RNA, and metagenomics
http://parts.igem.org/Main_Page
ERCC External RNA Control Consortium NIST
DNA
RNA
FDA
RSBP
10. Testing and benchmarking for RNA standards
(FDA’s SEQC and ABRF-NGS study)
RNA-seq Standards
Li, Tighe et al., Nature Biotechnology, Sept. 2014
SEQC Consortium, Nature Biotechnology, Sept. 2014
Li, Łabaj, Zumbo, et al., Nature Biotechnology, Sept. 2014http://www.nature.com/nbt/collections/seqc/index.html
11. Even with >12 billion reads, more genes
appear and are annotation/tool dependent.
http://www.nature.com/nbt/focus/seqc/index.html
12. Reference DNA,
TruSeq PCR-free 350
FFPE, TruSeq Nano
FFPE, TruSeq PCR-free
maternal
paternal
son
son
(Coriell)
A B C C2
Personal Genome Project
NIST Reference Human Genomes
C2f
Phase 2 DNA Samples: human
13. Ste Eco Pflu pool
%GC: 28 47 72
Reference bacterial genomes
TruSeq PCR-free 550
Phase 2 DNA Samples: bacterial
15. Lab 1
Compare NIST and Coriell stock cell culture genomes
Evaluate Coriell cell culture as an FFPE reference material
HiSeq X Ten, 2x150
1 flow cell
7 libraries
Library kits: TruSeq PCR Free and TruSeq Nano, 350 bp inserts
16. Lab 1
MiSeq v3, 2x300
Lab 2
Lab 3
3 flow cells
36 libraries
Lab 1
HiSeq 2500 v3 Rapid Run, 2x250
Lab 2
Lab 3
6 flow cells
45 libraries
Generate standardized human genome sequencing datasets
Measure intra- and inter-lab variation
Measure sequencing performance at GC composition extremes
Library kit: TruSeq PCR Free, 550 bp inserts for bacteria, 350 bp for sample C
17. Reference DNA,
AmpliSeq Exome
Ste Hah Mil pool
Samples
maternal
paternal
son
%GC: 28 47 72
A B C C2
Personal Genome Project
NIST Reference Human Genomes
Reference bacterial genomes
Ion Xpress Plus
Fragment Library
Life Technologies
18.
19. Measure sequencing performance at GC composition extremes
Measure intra- and inter-lab variation
Lab 1
RS II Sequel
Lab 2
Lab 3
Pacific Biosciences
20.
21. Samples and Platforms – All tested in triplicate across three distinct sites
Platform Human DNA Bacterial DNA
Illumina HiSeq X Ten A, B, C, C2, C2f
Illumina HiSeq 4000 A, B, C
Illumina HiSeq 2500 v4 1T A, B, C
Illumina HiSeq 2500 v3 Rapid Run C Ste, Eco, Mil, P
Illumina NextSeq 500 High Output C
Illumina MiSeq Ste, Eco, Mil, P
Life Tech Proton A, B, C exomes Ste, Eco, Mil, P
Life Tech S5 A, B, C exomes Ste, Eco, Mil, P
Life Tech PGM Ste, Eco, Mil, P
Pacific Biosciences Ste, Eco, Mil, P
Oxford Nanopore Ste, Eco, Mil, P
maternal
paternal
son
son
(Coriell)
A B C C2
Ste Eco Pflu pool
Human Trio Bacterial Isolates and Mixture
22. Sequencing summary
• 286/307 libraries have been sequenced
• Completion date for all data collection will be
August 2017
– First data is posted
– Submit manuscripts by October
• Data is being analyzed by a team of 25
bioinformatics specialist
– most are members of ABRF-NGS and GBIRG
– some are outside of ABRF
39. Dynamic, the Gut Is.
Measure it carefully, we must.
Aaron Del Duca
40. Ongoing efforts to reduce variance
(or embrace it when helpful)
Aaron Del Duca
41. 16S rRNA is only a part of the
erudition
Lan Y, Rosen G, Hershberg R. “Marker genes that are less conserved in their sequences are useful for predicting genome-
wide similarity levels between closely related prokaryotic strains.” Microbiome. 2016.
“16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes,
but not for closely related ones.”
42. Average Amino Acid identity (AAi) 16s rRNA
Escherichia/Shigella lineage is poorly defined by 16S
43. Metagenomics can expand the microbiome
to query across kingdoms
Data Type 16S 18S ITS Shotgun
Taxonomic Classification Yes Yes Yes Yes
Prokaryotes Yes No No Yes
Archaea Yes No No Yes
Eukaryotes No Yes Yes Yes
Parasites No Yes No Yes
Plasmids No No No Yes
Phages No No No Yes
Human Ancestry No No No Yes
Biosynthetic Gene Clusters No No No Yes
Antimicrobial Resistance (AMR) Markers No No No Yes
Kingdom Specificity Yes Yes Yes No
Approximate Raw Cost / Sample $100 $100 $125 $300
From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359768/
44. For complex metagenomic samples,
we see similar challenges as SEQC
Millions of Reads
NumberofSpecies
Elizabeth Hénaff
Abundance (MetaPhlAn)
55. • Sequins are synthetic DNA standards that ‘mirror’ and match the sequencing,
assembly and alignment of microbe genomes.
• Their synthetic sequence allows them to be added directly to a user’s DNA sample
prior to library preparation and sequencing, and thereby act as internal reference
controls.
W W W. S E Q U I N S . X Y Z
56. Diagnostic performance – assess the sensitivity and specificity for
detecting pathogens in a sample.
Quantitative accuracy – measure quantitative performance of a NGS
library, and the impact of sequence coverage on analysis (see over).
Sequins can be analyzed as internal controls throughout the NGS workflow:
Normalization – sequins can act as scaling factors to normalize between
multiple samples for more accurate comparisons.
Quality control and troubleshooting – calibrate and optimize library
preparation, sequencing and analysis steps.
W W W. S E Q U I N S . X Y Z
57. • Metaquins are titrated across a 105 –fold concentration range to form a quantitative
ladder.
• This ladder can be used to assess quantitative accuracy, sensitivity limits and the
impact of sequencing coverage on de novo assembly.
• Alternative mixtures can be used to assess fold-change differences between samples
W W W. S E Q U I N S . X Y Z
61. Genetics and Epigenetics of
Anti-microbial Resistance (AMR)
http://gcgh.grandchallenges.org/grant/global-distribution-and-epigenetic-stratification-antimicrobial-resistance
62.
63. Open, Transparent, Global Collaboration
3 Goals:
1. Geospatial Metagenomic and Forensic Maps
2. Anti-microbial resistance (AMR) marker tracking
3. New Biosynthetic Gene Clusters (BGCs); new drugs
www.metasub.org
89. StuckOnU
MetaSUB metagenomics research comes to the ABRF 2017 in San Diego!
Our research study investigates the microbiome and DNA of your cell phone, as part
of a global study on the genomics of our world’s cities.
121. Flight data shows very good accuracy (89-92%) for 2D reads
Plus, good read accuracy (76-79%) for 1D reads
for the template/complement measures.
Flight Data Read Accuracy(%ofreads)
122.
123. The first genome sequenced and
assembled from beyond-Earth reads
http://biorxiv.org/content/early/2016/09/27/077651
125. Direct Detection of Methylation on PacBio
70.5 71.0 71.5 72.0 72.5 73.0 73.5 74.0 74.5
0
100
200
300
400
Fluorescence
intensity(a.u.)
Time (s)
104.5 105.0 105.5 106.0 106.5 107.0 107.5 108.0 108.5
0
100
200
300
400
Fluorescence
intensity(a.u.)
Time (s)
C
T G A TC G T A C
mA
AG TCT A A
G C C A A A
A
Approach: Kinetic detection of methylated bases during SMRT DNA sequencing
Example: N6-methyladenosine (mA)
Flusberg et al, 2010
139. Conclusions
• Data sets are made and ready for most of the
FDA’s SEQC and ABRF-NGS DNA studies
• Epigenome QC (EpiQC) group is also testing the
same human and metagenone samples for base
modifications
• Metagenomics benchmarking shows striking
differences in default pipelines, even with similar
database sizes and coverage.
• Sequencing experiments can now be planned for
space flight. Maybe Mars.
140. Deep Gratitude to Many People:
Illumina
Gary Schroth
Marc Van Oene
Univ. Chicago
Yoav Gilad
FDA/SEQC/Fudan Univ.
Leming Shi
NIH/UDP/NCBI
Jean & Danielle Thierry-Mieg
Baylor
Jeff Rogers
MSKCC
Danwei Huangfu
Christina Leslie
Ross Levine
Alex Kentsis
HudsonAlpha
Shawn Levy
Mason Lab
Ebrahim Afshinnekoo
Sofia Ahsanuddin
Noah Alexander
Pradeep Ambrose
Daniela Bezdan
Marjan Bozinoski
Dhruva Chandramohan
Chou Chou
David Danko
Tim Donahoe
Jonathan Foox
Elizabeth Hénaff
Matthew MacKay
Alexa McIntyre
Cem Meyden
Niamh O’Hara
Lenore Pipes
Jake Reed
Heba Shabaan
Delia Tomoiaga
Priyanka Vijay
David Westfall
Cornell/WCM
Scott Blanchard
Selina Chen-Kiang
Olivier Elemento
Samie Jaffrey
Ari Melnick
Margaret Ross
Epigenomics Core
Duke
Stacy Horner
Nandan Gokhale
Icahn/MSSM
Eric Schadt,
Andrew Kasarskis,
Joel Dudley, Ali
Bashir,
Bobby Sebra
ABRF
George Grills
Scott Tighe
Don Baldwin
Miami
Maria E Figueroa
AMNH
George Amato
Mark Sidall
@mason_lab
NYU
Martin Blaser
Jane Carlton
Julia Maritz
Chris Park
MIT Media Lab
Kevin Slavin
Devora Najjar
Regina Flores
Rockefeller
Jeanne Garbarino
Charles Rice
NASA
Aaron Burton
Sarah Castro-Wallace
Kate Rubins
Graham Scott
Craig Kundrot
Jackson Labs
Sheng Li
UVA
Francine Garrett-Bakelman